Tall baseboard will not be flush with the wall all over and does need caulking to look right if you are painting it. As far as the nailing, I am not sure how many misses that they made, but that sounds unusual. Baseboard is so easy to nail in a properly framed building where the studs are at 16" on center. Trim carpenters place the tape measure down on the ground and then nail at the marked 16" intervals, and that usually gets 95% of the nails into the studs. It is not done haphazardly unless this was a complete hack by a drunken sailor. FYI, trim carpenters do not take as much time to cope joints and make perfect miters with painted trim for two reasons. First, if it is a cheap composite or laminated trim, the material does not work as well with typical trim carpenter techniques to tighten joints and miters (coping, filing sanding). Secondly, they know that there is a much wider margin for error because the trim will be caulked and painted, which usually hides 99% of the issues with nail holes, miter and joint separations, baseboard away fro walls in between studs, etc. Third, a really good painter is required for painted trim to look right. It needs a lot of work, and it should be spray painted to do it right.

We tried out Ace and Minwax stains on our pine windows (Sierra Pacific Windows). Light stains were: Puritan Pine by Minwax and Shaker Pine by Ace. Both were so light as to be barely discernable (to me) from just putting a clear poly coat on it (which we had done to a previously installed SP window). Medium stains were: Ace Early American and Minwax Early American. Ace's EA came out much lighter than Minwax's, which read more darker red-brown to me. Ace's EA was really pretty - lighter golden with a little red. We are going with Ace's EA for the windows. We also tried Minwax fruitwood and provincial. Fruitwood came out weirdly green for us. Provinical came out too dark for my taste. We have red oak floors (left natural, no stain, just water based poly or whatever they put on them). I opted to go with SW Dover White (creamy white) paint for our window trim and baseboards. I know - most people paint the window too, or use stained wood trim, but I couldn't for a few reasons: One, I really do like the look of the white trim around the nice wood window and I find the white trim to be crisper, brighter and easier to pair with paint colors. Second, we couldn't get (afford) anything but pine, and I tried the aforementioned stains on pine and ho boy, they came out super blotchy and streaky. And we used a pre-conditioner, it's just the way pine takes stain, I guess. Some boards were beautiful, others looked simply awful. My husbadn wanted wood, but I convinced him to go with white after the staining came out so erratically. Good luck to you! KPK ps - I'd also fool around with combining stains as that would probably work to tone down a darker color. Maybe try adding Minwax golden oak to the puritan pine - maybe it would beef it up a bit.

In my opinion, oil based primer and latex primer, if both are high quality, should bond equally well. The real reason I suggest using BIN is because it will bond better than both, plus it will kill the water stains. I'm guessing that you have water stains because that is what usually happens when condensation from the glass leaks onto the wood. With the sun coming through the glass panes, it is like a magnifying glass on an ant, which will cook the moisture that is sitting on your wood and it will not take long for that moisture to eat through any finish that is on the wood and then eat through the stain layer. This is why it is so important to have the humidity level set so that moisture does not collect on your glass panes. BIN is actually a shellac based product, which means it is not latex or oil based. You would clean your equipment with denatured alcohol, it dries super fast and is pretty smelly...probably stinks worse than oil based. It really sounds like you have some cheap windows to me. If you can't stop the condensation issue and the windows stick when you close them, these are signs. No paint is going to stick long term if a painted surface rubs against raw wood and also painted surfaces should never touch other painted surfaces. What you want is the painted surfaces of your windows touching weatherstips when they are closed tight. I would suggest sanding the windows until you can close them without wood rubbing against wood. I realize you may not be able to do this with every window because they may be too tight because of any number of reasons, but that is where I would start. What is the brand of the windows? Are they double hung style or crankout type casement windows?

Like jlc says, your plans don't seem to jive with the actual house. I would embrace the look you have and definitely don't make any decor plans until you've lived in it for a bit. Especially if the style is different from what you've been used to - it will take a while to adjust your thinking. If anything, I would consider painting out the doors and any window trim there is. The style of your house seems like it would make a great blank canvas for a wonderful eclectic look. But as I said, live with it a while before making any major plans.